Markers + reference

Caragana

23 species · Fabaceae · Fabales

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Species 23
Genome length 128–134 kb
Candidate markers 229
Primer pairs 70

Genome-wide nucleotide diversity

Sliding-window nucleotide diversity
Sliding-window nucleotide diversity (π) across the plastome.

Candidate markers

4 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 229 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps12-clpP Genome 677 0.1738 0.88 75.2 yes View details
rps19-rpl2 Genome 2066 0.3465 0.42 77.0 yes View details
rpl23-trnI-CAU Genome 1351 0.2335 0.38 67.9 yes View details
trnN-GUU-ycf1 Genome 760 0.1729 0.74 74.2 yes View details
atpH-atpF Genome 681 0.0425 0.94 83.8 yes View details
clpP Genome 1333 0.0641 0.94 77.6 yes View details
trnQ-UUG-accD Genome 612 0.0391 0.98 76.4 yes View details
rrn5-trnR-ACG Genome 322 0.0512 0.99 76.0 yes View details
trnG-UCC-trnS-GCU Genome 501 0.0164 1.00 75.8 yes View details
trnR-ACG-trnN-GUU Genome 625 0.0412 0.99 75.2 yes View details
trnL-CAA-trnT-UGU Genome 1534 0.0287 0.94 72.5 yes View details
ycf1-rps15 Genome 473 0.1038 0.98 71.2 yes View details
psbK-trnQ-UUG Genome 675 0.0329 0.98 70.2 yes View details
trnG-GCC-psbZ Genome 639 0.0427 0.97 69.2 yes View details
Candidate markers include all hotspot labels marked in the diversity plot, listed in genomic order, plus the top 10 remaining regions by MarkerSeek score. Primer design is attempted for every listed region. Primer available: yes means at least one valid primer pair was found; no means no valid pair passed screening; NA means primer design was skipped.

Primer pairs

Showing the top 30 of 70 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnL-CAA-trnT-UGU_p1 trnL-CAA-trnT-UGU ACCAATTTCGCCATATCCCC GCGATGCTCTAACCTCTGAG 1315–1771 1.000 90.9
trnL-CAA-trnT-UGU_p2 trnL-CAA-trnT-UGU TAGCGTCTACCAATTTCGCC GCGATGCTCTAACCTCTGAG 1323–1779 1.000 90.4
trnL-CAA-trnT-UGU_p3 trnL-CAA-trnT-UGU ACCAATTTCGCCATATCCCC GGAATCGAACCGATGACCAT 1347–1803 1.000 90.0
trnL-CAA-trnT-UGU_p4 trnL-CAA-trnT-UGU TAGCGTCTACCAATTTCGCC GGAATCGAACCGATGACCAT 1355–1811 1.000 89.5
trnL-CAA-trnT-UGU_p5 trnL-CAA-trnT-UGU CCCATTGTGAATTCCAGGGT GCGATGCTCTAACCTCTGAG 1408–1864 1.000 89.0
trnG-GCC-psbZ_p1 trnG-GCC-psbZ TACCATTCAACTATATCCGC AGTGGGTATTCTTAATTCTCTCA 526–708 1.000 52.0
trnG-GCC-psbZ_p2 trnG-GCC-psbZ TTACCATTCAACTATATCCGC AGTGGGTATTCTTAATTCTCTCA 527–709 1.000 52.0
trnG-GCC-psbZ_p3 trnG-GCC-psbZ TACCATTCAACTATATCCGC AGTGGGTATTCTTAATTCTCTCATCT 526–708 1.000 52.0
trnG-GCC-psbZ_p4 trnG-GCC-psbZ TTACCATTCAACTATATCCGC AGTGGGTATTCTTAATTCTCTCATCT 527–709 1.000 52.0
trnG-GCC-psbZ_p5 trnG-GCC-psbZ TTTACCATTCAACTATATCCGC AGTGGGTATTCTTAATTCTCTCA 528–710 1.000 52.0
atpH-atpF_p1 atpH-atpF CCGGAAGCAGAGGACAAAAT GATGGCCAGTAACTCAAGCA 769–848 1.000 89.7
atpH-atpF_p2 atpH-atpF CCGGAAGCAGAGGACAAAAT CGGATGGCCAGTAACTCAAG 771–850 1.000 87.9
atpH-atpF_p3 atpH-atpF AGCAGAGGACAAAATACGGG GATGGCCAGTAACTCAAGCA 764–843 1.000 87.9
atpH-atpF_p4 atpH-atpF CCGGAAGCAGAGGACAAAAT TGGCCAGTAACTCAAGCAAA 767–846 1.000 87.8
atpH-atpF_p5 atpH-atpF TGGGCTGGTTGTAGCATTAG GATGGCCAGTAACTCAAGCA 698–777 1.000 87.7
trnG-UCC-trnS-GCU_p1 trnG-UCC-trnS-GCU GGGGTCTATAGAACGAATCGC AATCCGACGCTTTAGTCCAC 484–618 1.000 82.8
trnG-UCC-trnS-GCU_p2 trnG-UCC-trnS-GCU ACGAATCGCACTTTTACCACT AATCCGACGCTTTAGTCCAC 472–606 1.000 81.3
trnG-UCC-trnS-GCU_p3 trnG-UCC-trnS-GCU GGGGTCTATAGAACGAATCGC ACGGAAAGAGAGGGATTCGA 538–672 1.000 81.0
trnG-UCC-trnS-GCU_p4 trnG-UCC-trnS-GCU GGGGTCTATAGAACGAATCGC CAATCCGACGCTTTAGTCCA 485–619 0.957 79.5
trnG-UCC-trnS-GCU_p5 trnG-UCC-trnS-GCU ACGAATCGCACTTTTACCACT CAATCCGACGCTTTAGTCCA 473–607 0.957 78.2
psbK-trnQ-UUG_p1 psbK-trnQ-UUG ACTTGAATAAAGGGCAGAGTGA GACCAAAACCCGTTGCCTTA 517–863 1.000 65.4
psbK-trnQ-UUG_p2 psbK-trnQ-UUG ACTTGAATAAAGGGCAGAGTGA CGAATAACGGGACCAAAACC 527–873 1.000 63.6
psbK-trnQ-UUG_p3 psbK-trnQ-UUG ACTTGAATAAAGGGCAGAGTGA ACCAAAACCCGTTGCCTTAC 516–862 1.000 63.1
psbK-trnQ-UUG_p4 psbK-trnQ-UUG ACTTGAATAAAGGGCAGAGTGAA GACCAAAACCCGTTGCCTTA 517–863 1.000 62.4
psbK-trnQ-UUG_p5 psbK-trnQ-UUG ACTTGAATAAAGGGCAGAGTG GACCAAAACCCGTTGCCTTA 517–863 1.000 61.5
trnQ-UUG-accD_p1 trnQ-UUG-accD GAGGTTCGAATCCTTCCGTC TCCTGAAATAATCAACATTGCTGT 654–713 0.957 50.9
trnQ-UUG-accD_p2 trnQ-UUG-accD GAGGTTCGAATCCTTCCGTC CCTGAAATAATCAACATTGCTGT 653–712 0.957 50.3
trnQ-UUG-accD_p3 trnQ-UUG-accD GAGGTTCGAATCCTTCCGTC TGTTCCTGAAATAATCAACATTGCT 657–716 0.957 50.3
trnQ-UUG-accD_p4 trnQ-UUG-accD GAGGTTCGAATCCTTCCGTC TTCCTGAAATAATCAACATTGCTGT 655–714 0.957 50.3
trnQ-UUG-accD_p5 trnQ-UUG-accD GAGGTTCGAATCCTTCCGTC CCGTATGTTCCTGAAATAATCAACA 662–721 0.957 50.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (23)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Caragana acanthophylla NC_077538.1 131599 View on NCBI ↗
Caragana arborescens NC_077537.1 129345 View on NCBI ↗
Caragana bongardiana NC_077536.1 129569 View on NCBI ↗
Caragana brachypoda NC_077535.1 132700 View on NCBI ↗
Caragana brevifolia NC_060689.1 132359 View on NCBI ↗
Caragana erinacea PV870771.1 133647 View on NCBI ↗
Caragana frutex NC_077534.1 131848 View on NCBI ↗
Caragana jubata PP848196.1 128458 View on NCBI ↗
Caragana korshinskii NC_035229.1 129331 View on NCBI ↗
Caragana kozlowii NC_035228.1 131274 View on NCBI ↗
Caragana leucophloea NC_077533.1 134240 View on NCBI ↗
Caragana liouana NC_077532.1 129507 View on NCBI ↗
Caragana microphylla NC_032691.1 130029 View on NCBI ↗
Caragana opulens NC_073541.1 131946 View on NCBI ↗
Caragana pruinosa NC_077531.1 129597 View on NCBI ↗
Caragana purdomii NC_077530.1 129546 View on NCBI ↗
Caragana roborovskyi NC_058649.1 129112 View on NCBI ↗
Caragana rosea NC_077529.1 128168 View on NCBI ↗
Caragana stenophylla NC_057610.1 132895 View on NCBI ↗
Caragana tangutica OR491701.1 128445 View on NCBI ↗
Caragana tibetica NC_073542.1 129303 View on NCBI ↗
Caragana tragacanthoides NC_077528.1 129038 View on NCBI ↗
Caragana turkestanica NC_081909.1 129453 View on NCBI ↗